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hiReadsProcessor (version 1.8.2)

Functions to process LM-PCR reads from 454/Illumina data

Description

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

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Version

Version

1.8.2

License

GPL-3

Maintainer

Nirav V Malani

Last Published

February 15th, 2017

Functions in hiReadsProcessor (1.8.2)

Add a specific feature/attribute to the sampleInfo object.

Extract a specific feature/attribute of the sampleInfo object.

getIntegrationSites

Obtain integration sites from BLAT output

Read PSL file(s) outputted by BLAT

Bin values or make ISUs by assigning a unique ID to them within discrete factors.

Find the 3' linkers and add results to SampleInfo object.

addListNameToReads

Prepend name attribute of a list to DNAStringSet

Remove values/positions which are overlapping between discrete groups based on their frequency.

findIntegrations

Find the integration sites and add results to SampleInfo object.

Return PSL file columns with classes

primerIDAlignSeqs

Align a short pattern with PrimerID to variable length target sequences.

Find the 5' primers and add results to SampleInfo object.

Find vector DNA in reads and add results to SampleInfo object.

Extract sequences for a feature in the sampleInfo object.

Bin values or make OTUs by assigning a unique ID to them within discrete factors.

Test if pattern aligns better in +/- orientation.

Calculate breakpoint/sonic abundance of integration sites in a population

removeReadsWithNs

Remove sequences with ambiguous nucleotides.

Write PSL file from dataframe or GRanges

read.seqsFromSector

Read fasta/fastq/sff given the path or sampleInfo object.

Breaks an object into chunks of N size.

Reads a BAM/SAM file and converts it into a PSL like format.

Sample Integration Sites Sequencing Data

Split DNAStringSet object using first X number of bases defined by a vector.

vpairwiseAlignSeqs

Align a short pattern to variable length target sequences.

Align a listed DNAStringSet to a reference using gfClient or standalone BLAT.

Start/Stop a gfServer instance

write.listedDNAStringSet

Write a fasta file per sample in parallel

getSectorsForSamples

Get sectors for samples defined in the sampleInfo object.

Simple summary of a sampleInfo object.

Find and trim a short pattern sequence from the subject.

Demultiplex reads by their barcodes

hiReadsProcessor

Functions to process LM-PCR reads from 454/Illumina data

pslToRangedObject

Convert psl dataframe to GRanges

pairwiseAlignSeqs

Align a short pattern to variable length target sequences.

Read contents of a sequencing folder and make a SimpleList object

Replicate sequences from DNAStringSet object using counts identifier or vector

Read blast8 file(s) outputted by BLAT

findAndRemoveVector

Find and trim vector sequence from reads.

pairUpAlignments

Pair up alignments in a GRanges object

dereplicateReads

Removes duplicate sequences from DNAStringSet object.

read.sampleInfo

Read a sample information file and format appropriate metadata.

Cluster/Correct values within a window based on their frequency given discrete factors

PSL file output

Find the 5' LTRs and add results to SampleInfo object.

Align sequences using BLAT.

splitSeqsToFiles

Split DNA sequences into smaller files.

Trim sequences from a specific side.

troubleshootLinkers

Compare LTRed/Primed sequences to all linkers.

Find the 5' primers and add results to SampleInfo object.